X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=37b4dac5b5b17f5101e4dcdb21b2e239542aa73f;hp=ca4f84e53a4e4da494d3334a3b4d349b590cf7cc;hb=3da878124135ff033f42d19d8733891b09e953cd;hpb=549cdd8bcac48cade7880c4a800d9c90b4d02632 diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index ca4f84e..37b4dac 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -28,7 +28,6 @@ import jalview.analysis.TreeModel; import jalview.analysis.scoremodels.ScoreModels; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; -import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; @@ -41,11 +40,12 @@ import jalview.datamodel.NodeTransformI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; +import jalview.gui.ImageExporter.ImageWriterI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.NewickFile; import jalview.jbgui.GTreePanel; -import jalview.util.ImageMaker; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -53,14 +53,13 @@ import java.awt.Font; import java.awt.Graphics; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; +import java.io.File; import java.io.FileOutputStream; import java.util.ArrayList; import java.util.List; -import javax.imageio.ImageIO; import javax.swing.ButtonGroup; import javax.swing.JMenuItem; import javax.swing.JRadioButtonMenuItem; @@ -126,6 +125,7 @@ public class TreePanel extends GTreePanel public AlignmentViewport getViewPort() { + // @Mungo - Why don't we return our own viewport ??? return getTreeCanvas().getViewport(); } @@ -133,12 +133,12 @@ public class TreePanel extends GTreePanel NewickFile newTree, AlignmentView inputData) { - setViewport(ap.av); + av = ap.av; this.treeType = type; this.scoreModelName = modelName; treeCanvas = new TreeCanvas(this, ap, scrollPane); - scrollPane.setViewportView(getTreeCanvas()); + scrollPane.setViewportView(treeCanvas); PaintRefresher.Register(this, ap.av.getSequenceSetId()); @@ -155,9 +155,9 @@ public class TreePanel extends GTreePanel @Override public void internalFrameClosed(InternalFrameEvent evt) { - if (getViewport() != null) + if (av != null) { - getViewport().removePropertyChangeListener(listener); + av.removePropertyChangeListener(listener); } } }); @@ -194,13 +194,13 @@ public class TreePanel extends GTreePanel } tree.updatePlaceHolders((List) evt.getNewValue()); - getTreeCanvas().nameHash.clear(); // reset the mapping between canvas + treeCanvas.nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); } } }; - getViewport().addPropertyChangeListener(listener); + av.addPropertyChangeListener(listener); return listener; } @@ -213,7 +213,7 @@ public class TreePanel extends GTreePanel void buildAssociatedViewMenu() { AlignmentPanel[] aps = PaintRefresher - .getAssociatedPanels(getViewport().getSequenceSetId()); + .getAssociatedPanels(av.getSequenceSetId()); if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); @@ -237,16 +237,17 @@ public class TreePanel extends GTreePanel for (i = 0; i < iSize; i++) { final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.getViewName(), ap == getTreeCanvas().getAssociatedPanel()); + item = new JRadioButtonMenuItem(ap.av.getViewName(), + ap == treeCanvas.getAssociatedPanel()); buttonGroup.add(item); item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - getTreeCanvas().applyToAllViews = false; - getTreeCanvas().setAssociatedPanel(ap); - getTreeCanvas().setViewport(ap.av); + treeCanvas.applyToAllViews = false; + treeCanvas.setAssociatedPanel(ap); + treeCanvas.setViewport(ap.av); PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); @@ -257,13 +258,13 @@ public class TreePanel extends GTreePanel final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem( MessageManager.getString("label.all_views")); buttonGroup.add(itemf); - itemf.setSelected(getTreeCanvas().applyToAllViews); + itemf.setSelected(treeCanvas.applyToAllViews); itemf.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - getTreeCanvas().applyToAllViews = itemf.isSelected(); + treeCanvas.applyToAllViews = itemf.isSelected(); } }); associateLeavesMenu.add(itemf); @@ -296,7 +297,7 @@ public class TreePanel extends GTreePanel if (newtree != null) { - tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata, + tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, newtree); if (tree.getOriginalData() == null) { @@ -306,20 +307,21 @@ public class TreePanel extends GTreePanel else { ScoreModelI sm = ScoreModels.getInstance() - .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel()); + .getScoreModel(scoreModelName, + treeCanvas.getAssociatedPanel()); TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) - ? new NJTree(getViewport(), sm, similarityParams) - : new AverageDistanceTree(getViewport(), sm, similarityParams); + ? new NJTree(av, sm, similarityParams) + : new AverageDistanceTree(av, sm, similarityParams); tree = new TreeModel(njtree); showDistances(true); } tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); - getTreeCanvas().setTree(tree); - getTreeCanvas().repaint(); - getViewport().setCurrentTree(tree); - if (getViewport().getSortByTree()) + treeCanvas.setTree(tree); + treeCanvas.repaint(); + av.setCurrentTree(tree); + if (av.getSortByTree()) { sortByTree_actionPerformed(); } @@ -328,20 +330,20 @@ public class TreePanel extends GTreePanel public void showDistances(boolean b) { - getTreeCanvas().setShowDistances(b); + treeCanvas.setShowDistances(b); distanceMenu.setSelected(b); } public void showBootstrap(boolean b) { - getTreeCanvas().setShowBootstrap(b); + treeCanvas.setShowBootstrap(b); bootstrapMenu.setSelected(b); } public void showPlaceholders(boolean b) { placeholdersMenu.setState(b); - getTreeCanvas().setMarkPlaceholders(b); + treeCanvas.setMarkPlaceholders(b); } /** @@ -390,6 +392,7 @@ public class TreePanel extends GTreePanel @Override public void saveAsNewick_actionPerformed(ActionEvent e) { + // TODO: JAL-3048 save newick file for Jalview-JS JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); @@ -432,7 +435,7 @@ public class TreePanel extends GTreePanel public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems - getTreeCanvas().startPrinting(); + treeCanvas.startPrinting(); } @Override @@ -456,7 +459,7 @@ public class TreePanel extends GTreePanel { // we try to get the associated view's gap character // but this may fail if the view was closed... - gc = getViewport().getGapCharacter(); + gc = av.getGapCharacter(); } catch (Exception ex) { @@ -469,8 +472,8 @@ public class TreePanel extends GTreePanel // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); - AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null) - ? getViewport().getAlignment().getDataset() + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() : null; if (dataset != null) { @@ -507,7 +510,7 @@ public class TreePanel extends GTreePanel @Override public void fitToWindow_actionPerformed(ActionEvent e) { - getTreeCanvas().fitToWindow = fitToWindow.isSelected(); + treeCanvas.fitToWindow = fitToWindow.isSelected(); repaint(); } @@ -520,15 +523,15 @@ public class TreePanel extends GTreePanel public void sortByTree_actionPerformed() { - if (getTreeCanvas().applyToAllViews) + if (treeCanvas.applyToAllViews) { final ArrayList commands = new ArrayList<>(); for (AlignmentPanel ap : PaintRefresher - .getAssociatedPanels(getViewport().getSequenceSetId())) + .getAssociatedPanels(av.getSequenceSetId())) { commands.add(sortAlignmentIn(ap.av.getAlignPanel())); } - getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI() + av.getAlignPanel().alignFrame.addHistoryItem(new CommandI() { @Override @@ -563,7 +566,7 @@ public class TreePanel extends GTreePanel } }); for (AlignmentPanel ap : PaintRefresher - .getAssociatedPanels(getViewport().getSequenceSetId())) + .getAssociatedPanels(av.getSequenceSetId())) { // ensure all the alignFrames refresh their GI after adding an undo item ap.alignFrame.updateEditMenuBar(); @@ -571,8 +574,9 @@ public class TreePanel extends GTreePanel } else { - getTreeCanvas().getAssociatedPanel().alignFrame - .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel())); + treeCanvas.getAssociatedPanel().alignFrame + .addHistoryItem( + sortAlignmentIn(treeCanvas.getAssociatedPanel())); } } @@ -599,7 +603,7 @@ public class TreePanel extends GTreePanel @Override public void font_actionPerformed(ActionEvent e) { - if (getTreeCanvas() == null) + if (treeCanvas == null) { return; } @@ -609,14 +613,14 @@ public class TreePanel extends GTreePanel public Font getTreeFont() { - return getTreeCanvas().font; + return treeCanvas.font; } public void setTreeFont(Font f) { - if (getTreeCanvas() != null) + if (treeCanvas != null) { - getTreeCanvas().setFont(f); + treeCanvas.setFont(f); } } @@ -629,7 +633,7 @@ public class TreePanel extends GTreePanel @Override public void distanceMenu_actionPerformed(ActionEvent e) { - getTreeCanvas().setShowDistances(distanceMenu.isSelected()); + treeCanvas.setShowDistances(distanceMenu.isSelected()); } /** @@ -641,7 +645,7 @@ public class TreePanel extends GTreePanel @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { - getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected()); + treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); } /** @@ -653,130 +657,31 @@ public class TreePanel extends GTreePanel @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { - getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected()); + treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Outputs the Tree in image format (currently EPS or PNG). The user is + * prompted for the file to save to, and for EPS (unless a preference is + * already set) for the choice of Text or Lineart for character rendering. */ @Override - public void epsTree_actionPerformed(ActionEvent e) + public void writeTreeImage(TYPE imageFormat) { - boolean accurateText = true; - - String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING", - "Prompt each time"); - - // If we need to prompt, and if the GUI is visible then - // Prompt for EPS rendering style - if (renderStyle.equalsIgnoreCase("Prompt each time") - && !(System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true"))) - { - EPSOptions eps = new EPSOptions(); - renderStyle = eps.getValue(); - - if (renderStyle == null || eps.cancelled) - { - return; - } - - } - - if (renderStyle.equalsIgnoreCase("text")) + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); + ImageWriterI writer = new ImageWriterI() { - accurateText = false; - } - - int width = getTreeCanvas().getWidth(); - int height = getTreeCanvas().getHeight(); - - try - { - JalviewFileChooser chooser = new JalviewFileChooser( - ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.create_eps_from_tree")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value != JalviewFileChooser.APPROVE_OPTION) - { - return; - } - - Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream( - chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, - height); - - pg.setAccurateTextMode(accurateText); - - getTreeCanvas().draw(pg, width, height); - - pg.flush(); - pg.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void pngTree_actionPerformed(ActionEvent e) - { - int width = getTreeCanvas().getWidth(); - int height = getTreeCanvas().getHeight(); - - try - { - JalviewFileChooser chooser = new JalviewFileChooser( - ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); - - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.create_png_from_tree")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + @Override + public void exportImage(Graphics g) throws Exception { - return; + treeCanvas.draw(g, width, height); } - - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream( - chooser.getSelectedFile()); - - BufferedImage bi = new BufferedImage(width, height, - BufferedImage.TYPE_INT_RGB); - Graphics png = bi.getGraphics(); - - getTreeCanvas().draw(png, width, height); - - ImageIO.write(bi, "png", out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } + }; + String tree = MessageManager.getString("label.tree"); + ImageExporter exporter = new ImageExporter(writer, null, imageFormat, + tree); + exporter.doExport(null, this, width, height, tree.toLowerCase()); } /** @@ -804,20 +709,20 @@ public class TreePanel extends GTreePanel if (sq != null) { // search dbrefs, features and annotation - DBRefEntry[] refs = jalview.util.DBRefUtils + List refs = jalview.util.DBRefUtils .selectRefs(sq.getDBRefs(), new String[] { labelClass.toUpperCase() }); if (refs != null) { - for (int i = 0; i < refs.length; i++) + for (int i = 0, ni = refs.size(); i < ni; i++) { if (newname == null) { - newname = new String(refs[i].getAccessionId()); + newname = new String(refs.get(i).getAccessionId()); } else { - newname = newname + "; " + refs[i].getAccessionId(); + newname += "; " + refs.get(i).getAccessionId(); } } } @@ -884,6 +789,36 @@ public class TreePanel extends GTreePanel return ttl; } + /** + * Builds an EPS image and writes it to the specified file. + * + * @param outFile + * @param textOption + * true for Text character rendering, false for Lineart + */ + protected void writeEpsFile(File outFile, boolean textOption) + { + try + { + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); + + FileOutputStream out = new FileOutputStream( + outFile); + EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, + height); + pg.setAccurateTextMode(!textOption); + treeCanvas.draw(pg, width, height); + + pg.flush(); + pg.close(); + } catch (Exception ex) + { + System.err.println("Error writing tree as EPS"); + ex.printStackTrace(); + } + } + public AlignViewport getViewport() { return av;